A federal judge has signed off on the smaller of two insider-trading settlements by hedge fund SAC Capital Advisors LP, even as one of its most senior employees faces criminal charges in the matter, according to court documents.

SAC unit Sigma Capital agreed last month to pay $14 million to settle allegations by the Securities and Exchange Commission that an analyst obtained inside information about technology companies Dell Inc. and Nvidia Corp. and passed it along to two portfolio managers at SAC, resulting in more than...